This is because the hobbit people appear to have been a lineage - ie an evolved species; you can tell this because their anatomy is consistent across multiple individuals. This suggests that their body shape was determined genetically. This could not be the consequence of Zika, or a similar virus, because these agents do not alter the DNA code of an individual. Instead they damage developing tissue; the brain is a major focus because its complexity means that cells there are growing very fast, making them relatively more vulnerable to damage compared with some other tissues. The consequence is a smaller-than normal brain, or microcephaly.

However, it is not clear if the link is real or not - there are some prospective studies underway, monitoring pregnant women before they get exposed to Zika virus.

Microcephaly is a tragedy. It's not normally something you would talk much about, but when it's in the news, every case is news. It is not clear that there is an actual increase in microcephaly, as the clinical definition is apparently a bit fuzzy. When microcephaly is in the news, it is something that people will actively look for.

When skulls of H. floresiensis or hobbits were first discovered there was debate over whether they were a new species or were individuals with microcephaly or some kind of endemic cretinism. I think the consensus is that they are not examples of pathological microcephally.

There is though a possible connection between the genes that are effected in the disorder microcephally and genes that may have been responsible for expanded brains in human evolution. In the book Ancestors in Our Genome, Eugene Harris says;

"Four such candidate genes are ASPM, MCPH1, CENPJ, and CDK5RAP2. Defects in these genes are known to be associated with the disorder microcephaly, in which individuals have a small head size and a severely underdeveloped cortex of the brain. This led researchers to surmise that these genes might be responsible for the expansion of the brain and increased cognition in human evolution. The functional link between the microcephaly genes and brains has been strengthened by the results of two different studies- one studying genes in a Norwegian population and the other in a Chinese population - that found that DNA variants in the genes are associated with differences among people in either cranial volume or the amount of surface area of the brain's cortex.

In evolutionary studies these genes were found to have adaptive signitures. Over the course of human evolution some of the microcephaly genes experienced an increased rate of change at functional DNA sites. And accelerated change also appears to have happened earlier in our evolutionary past on stem lineage that led to the entire ape and human group. More over adaptive change in these genes does not seem to have been restricted to the lineage leading to apes and humans, but is also found more widely across the so-called higher primate group, which also includes South american and African monkeys. One thing that seems to becoming clear is that the evolution of the human brain was primed by earlier adaptive evolution in our deeper primate ancestors, lending support to Darwin's assertion that the human brain (and mind) shows continuity with other primates, especialy apes. Strikingly, some of the microcephaly genes that appear to underlie increased brain size in humans also show signs of adaptive evolution on other branches of the primate tree where certain species have notably larger brains. This underscores another important point: there may be limited evolutionary means among different species to arrive at big brains."

I don't know how Homo floresiensis fits into all of this, but they may have had variants in these genes. Wikipedia says "In 2013, a comparison of the LB1 (hobbit) endocast to a set of 100 normocephalic and 17 microcephalic endocasts by Vannucci, Baron and Holloway showed that there is a wide variation in microcephalic brain shape ratios and that in these ratios the group as such is not clearly distinct from normocephalics. The LB1 brain shape nevertheless aligns slightly better with the microcephalic sample, with the shape at the extreme edge of the normocephalic group.[67]

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